I have list of genes and I would like to retrieve informations about mutations and especially the frequency of each mutation related to specific disease. I would like to use COSMIC database since I work with somatic mutations. I have seen the cosmic 67 package but it looks pretty old.

Any package or solution to suggest?

Thank you

Marco

They changed their license recently (https://cancer.sanger.ac.uk/cosmic/license), so you need to register and accept their license. Once you have the VCF, you can use the VariantAnnotation package to retrieve Cosmic annotation for you somatic calls, e.g.:

    vcf <- readVcf("your.vcf", "hg19")   

    cosmicSeqStyle <- seqlevelsStyle(headerTabix(TabixFile(cosmic.vcf.file))$seqnames)

    vcfRenamedSL <- vcf
    if (!length(intersect(seqlevelsStyle(vcf), cosmicSeqStyle))) {
        seqlevelsStyle(vcfRenamedSL) <- cosmicSeqStyle[1]
    }

    # look-up the variants in COSMIC, specify all the info/fixed/geno fields you need. vcf needs to be bgzip'ed and tabix'ed

    cosmic.vcf <- readVcf(cosmic.vcf.file, genome="hg19",  
        ScanVcfParam(which = rowRanges(vcfRenamedSL),
            info="CNT",
            fixed="ALT",
            geno=NA
        )
    )